fix: tidy up 0.9.2 merge, mostly label corrections

src/dewret/__main__.py

@@ -32,6 +32,7 @@
 import json
 
 from .core import set_configuration, set_render_configuration
+from .utils import load_module_or_package
 from .render import get_render_method, RawRenderModule, StructuredRenderModule
 from .tasks import Backend, construct
 
@@ -130,21 +131,8 @@ def _opener(key, mode):
         opener = _opener
 
     render = get_render_method(render_module, pretty=pretty)
-    workflow_init = workflow_py.parent
     pkg = "__workflow__"
-
-    # Try to import the workflow as a package, if possible, to allow relative imports.
-    try:
-        spec = importlib.util.spec_from_file_location(pkg, str(workflow_py.parent / "__init__.py"))
-        if spec is None or spec.loader is None:
-            raise ImportError(f"Could not open {pkg} package")
-        module = importlib.util.module_from_spec(spec)
-        sys.modules[pkg] = module
-        spec.loader.exec_module(module)
-        workflow = importlib.import_module(f"{pkg}.{workflow_py.stem}", pkg)
-    except ImportError:
-        loader = importlib.machinery.SourceFileLoader(pkg, str(workflow_py))
-        workflow = loader.load_module()
+    workflow = load_module_or_package(pkg, workflow_py)
     task_fn = getattr(workflow, task)
 
     try:

src/dewret/render.py

@@ -8,6 +8,7 @@
 from .workflow import Workflow, NestedStep
 from .core import RawType
 from .workflow import Workflow
+from .utils import load_module_or_package
 
 RenderConfiguration = TypeVar("RenderConfiguration", bound=dict[str, Any])
 
@@ -34,13 +35,7 @@ def get_render_method(renderer: Path | RawRenderModule | StructuredRenderModule,
 
         # Attempt to load renderer as package, falling back to a single module otherwise.
         # This enables relative imports in renderers and therefore the ability to modularize.
-        try:
-            loader = importlib.machinery.SourceFileLoader("__renderer__", str(renderer.parent / "__init__.py"))
-            sys.modules["__renderer__"] = loader.load_module(f"__renderer__")
-            render_module = importlib.import_module(f"__renderer__.{renderer.stem}", "__renderer__")
-        except ImportError:
-            loader = importlib.machinery.SourceFileLoader("__renderer__", str(renderer))
-            render_module = loader.load_module()
+        render_module = load_module_or_package("__renderer__", renderer)
         sys.modules["__renderer_mod__"] = render_module
     else:
         render_module = renderer

src/dewret/utils.py

@@ -20,8 +20,11 @@
 import hashlib
 import json
 import sys
-from types import FrameType, TracebackType, UnionType
+import importlib
+import importlib.util
+from types import FrameType, TracebackType, UnionType, ModuleType
 from typing import Any, cast, Union, Protocol, ClassVar, Callable, Iterable, get_args, get_origin, Annotated
+from pathlib import Path
 from collections.abc import Sequence, Mapping
 from sympy import Basic, Integer, Float, Rational
 
@@ -58,6 +61,24 @@ def make_traceback(skip: int = 2) -> TracebackType | None:
         frame = frame.f_back
     return tb
 
+def load_module_or_package(target_name: str, path: Path) -> ModuleType:
+    # Try to import the workflow as a package, if possible, to allow relative imports.
+    try:
+        spec = importlib.util.spec_from_file_location(target_name, str(path.parent / "__init__.py"))
+        if spec is None or spec.loader is None:
+            raise ImportError(f"Could not open {path.parent} package")
+        module = importlib.util.module_from_spec(spec)
+        sys.modules[target_name] = module
+        spec.loader.exec_module(module)
+        workflow = importlib.import_module(f"{target_name}.{path.stem}", target_name)
+    except ImportError as exc:
+        spec = importlib.util.spec_from_file_location(target_name, str(path))
+        if spec is None or spec.loader is None:
+            raise ImportError(f"Could not open {path} module") from exc
+        workflow = importlib.util.module_from_spec(spec)
+        spec.loader.exec_module(workflow)
+
+    return workflow
 
 def flatten_if_set(value: Any) -> RawType | Unset:
     """Takes a Raw-like structure and makes it RawType or Unset.

tests/test_annotations.py

@@ -70,15 +70,15 @@ def test_at_render() -> None:
         inputs:
           increment-1-num:
             default: 3
-            label: increment-1-num
+            label: num
             type: int
         outputs:
           out:
             label: out
             outputSource: to_int-1/out
             type:
             - int
-            - double
+            - float
         steps:
           increment-1:
             in:
@@ -108,15 +108,15 @@ def test_at_render() -> None:
         inputs:
           increment-1-num:
             default: 3
-            label: increment-1-num
+            label: num
             type: int
         outputs:
           out:
             label: out
             outputSource: to_int-1/out
             type:
             - int
-            - double
+            - float
         steps:
           increment-1:
             in:

tests/test_cwl.py

@@ -86,7 +86,7 @@ def get_now() -> datetime:
           days_in_future-1-num:
             default: 3
             type: int
-            label: days_in_future-1-num
+            label: num
           get_now-1:
             label: get_now-1
             type: datetime
@@ -115,7 +115,7 @@ def get_now() -> datetime:
           days_in_future-1-num:
             default: 3
             type: int
-            label: days_in_future-1-num
+            label: num
         outputs:
           out:
             label: out
@@ -154,7 +154,7 @@ def test_cwl_with_parameter() -> None:
         class: Workflow
         inputs:
           increment-{hsh}-num:
-            label: increment-{hsh}-num
+            label: num
             type: int
             default: 3
         outputs:
@@ -171,7 +171,7 @@ def test_cwl_with_parameter() -> None:
             out: [out]
     """)
 
-def test_cwl_with_parameter() -> None:
+def test_cwl_with_positional_parameter() -> None:
     """Check whether we can move raw input to parameters.
 
     Produces CWL for a call with a changeable raw value, that is converted
@@ -191,7 +191,7 @@ def test_cwl_with_parameter() -> None:
         class: Workflow
         inputs:
           increment-{hsh}-num:
-            label: increment-{hsh}-num
+            label: num
             type: int
             default: 3
         outputs:
@@ -357,14 +357,14 @@ def test_cwl_references() -> None:
         class: Workflow
         inputs:
           increment-{hsh_increment}-num:
-            label: increment-{hsh_increment}-num
+            label: num
             type: int
             default: 3
         outputs:
           out:
             label: out
             outputSource: double-{hsh_double}/out
-            type: 
+            type:
             - int
             - float
         steps:
@@ -397,14 +397,14 @@ def test_complex_cwl_references() -> None:
         class: Workflow
         inputs:
           increment-1-num:
-            label: increment-1-num
+            label: num
             type: int
             default: 23
         outputs:
           out:
             label: out
             outputSource: sum-1/out
-            type: 
+            type:
             - int
             - float
         steps:
@@ -459,7 +459,7 @@ def test_cwl_with_subworkflow_and_raw_params() -> None:
             type: int
           sum-1-right:
             default: 3
-            label: sum-1-right
+            label: right
             type: int
         outputs:
           out:
@@ -548,8 +548,7 @@ def test_tuple_floats() -> None:
     """
     result = tuple_float_return()
     workflow = construct(result, simplify_ids=True)
-    rendered = render(workflow)
-    print(yaml.dump(rendered))
+    rendered = render(workflow)["__root__"]
     assert rendered == yaml.safe_load("""
         cwlVersion: 1.2
         class: Workflow
@@ -558,11 +557,10 @@ def test_tuple_floats() -> None:
           out:
             label: out
             outputSource: tuple_float_return-1/out
-            type: 
-              items: 
-                - type: float
-                - type: float
-              type: array
+            items:
+              - float
+              - float
+            type: array
         steps:
           tuple_float_return-1:
             run: tuple_float_return

tests/test_fieldable.py

@@ -44,7 +44,7 @@ def test_fields_of_parameters_usable() -> None:
           outputSource: sum-1-1/out
           type:
           - int
-          - double
+          - float
       steps:
         sum-1-1:
           in:
@@ -83,7 +83,7 @@ class MyDataclass:
             outputSource: sum-1/out
             type:
             - int
-            - double
+            - float
         steps:
           sum-1:
             in:

tests/test_multiresult_steps.py

@@ -287,8 +287,9 @@ def test_pair_can_be_returned_from_step() -> None:
 
 def test_list_can_be_returned_from_step() -> None:
     """Tests whether a task can insert result fields into other steps."""
-    workflow = construct(list_cast(iterable=algorithm_with_pair()), simplify_ids=True)
-    rendered = render(workflow)["__root__"]
+    with set_configuration(flatten_all_nested=True):
+        workflow = construct(list_cast(iterable=algorithm_with_pair()), simplify_ids=True)
+        rendered = render(workflow)["__root__"]
 
     assert rendered == yaml.safe_load("""
         class: Workflow

tests/test_nested.py

@@ -26,14 +26,14 @@ def test_can_supply_nested_raw():
           pi:
             default: 3.141592653589793
             label: pi
-            type: double
+            type: float
         outputs:
           out:
             label: out
             outputSource: max_list-1/out
             type:
             - int
-            - double
+            - float
         steps:
           max_list-1:
             in:

tests/test_parameters.py

@@ -34,7 +34,7 @@ def test_cwl_parameters() -> None:
             type: int
             default: 3
           rotate-1-num:
-            label: rotate-1-num
+            label: num
             type: int
             default: 3
         outputs:
@@ -77,7 +77,7 @@ def test_complex_parameters() -> None:
             type: int
             default: 23
           rotate-2-num:
-            label: rotate-2-num
+            label: num
             type: int
             default: 23
         outputs: